She was frequently regarded as one of the powers behind the throne during her husband's 20-year presidency, and her family connections to powerful Hutu politicians are often regarded as having provided necessary political capital for Habyarimana. She was the centre of a powerful clique of northern Hutus called le clan de madame or akazu (Kinyarwanda for "little house").

Agathe Habyarimana is the sister of Protais Zigiranyirazo, who was implicated in the genocide. She was denied political asylum in France on January 4, 2007, but remained in France. She was arrested on Tuesday, March 2, 2010 following French President Nicolas Sarkozy's visit to Rwanda where he admitted to mistakes made by France over the genocide, further stating that France would seek out those responsible for the genocide who were living in France.

In September 2011, a French court denied Rwanda extradition of Habyarimana. A civil suit, perhaps thus weakened, remains.[5]